Wild canids and the ecological traps facing the climate change and deforestation in the Amazon Forest.

Ecological traps occur when species choose to settle in lower-quality habitats, even if this reduces their survival or productivity. This happens in situations of drastic environmental changes, resulting from anthropogenic pressures. In long term, this could mean the extinction of the species. We investigated the dynamics of occurrence and distribution of three canid species (Atelocynus microtis, Cerdocyon thous, and Spheotos venaticus) considering human threats to their habitats in the Amazon Rainforest. We analyzed the environmental thresholds for the occurrence of these species and related to the future projections of climatic niches for each one. All three species will be negatively affected by climate change in the future, with losses of up to 91% of the suitable area of occurrence in the Brazilian Amazon. A. microtis appear to be more forest-dependent and must rely on the goodwill of decision-makers to be maintained in the future. For C. thous and S. venaticus, climatic variables and those associated with anthropogenic disturbances that modulate their niches today may not act the same way in the future. Even though C. thous is least dependent on the Amazon Forest; this species may be affected in the future due to the ecological traps. S. venaticus, can also undergo the same process, but perhaps more drastically due to the lower ecological plasticity of this species compared to C. thous. Our results suggest that the ecological traps may put these two species at risk in the future. Using the canid species as a model, we had the opportunity to investigate these ecological effects that can affect a large part of the Amazonian fauna in the current scenario. Considering the high degree of environmental degradation and deforestation in the Amazon Rainforest, the theory of ecological traps must be discussed at the same level as the habitat loss, considering the strategies for preserving the Amazon biodiversity.

Novel insights on aquatic mammal MHC evolution: Evidence from manatee DQB diversity.

The low diversity in marine mammal major histocompatibility complex (MHC) appears to support the hypothesis of reduced pathogen selective pressure in aquatic systems compared to terrestrial environments. However, the lack of characterization of the aquatic and evolutionarily distant Sirenia precludes drawing more generalized conclusions. Therefore, we aimed to characterize the MHC DQB diversity of two manatee species and compare it with those reported for marine mammals. Our results identified 12 and 6 alleles in T. inunguis and T. manatus, respectively. Alleles show high rates of nonsynonymous substitutions, suggesting loci are evolving under positive selection. Among aquatic mammals, Pinnipeda DQB had smaller numbers of alleles, higher synonymous substitution rate, and a dN/dS ratio closer to 1, suggesting it may be evolving under more relaxed selection compared to fully aquatic mammals. This contradicts one of the predictions of the hypothesis that aquatic environments impose reduced pathogen pressure to mammalian immune system. These results suggest that the unique evolutionary trajectories of mammalian MHC may impose challenges in drawing ecoevolutionary conclusions from comparisons across distant vertebrate lineages.

TLR4 and TLR8 variability in Amazonian and West Indian manatee species from Brazil.

Amazonian (Trichechus inunguis) and West Indian (Trichechus manatus) manatees are aquatic mammals vulnerable to extinction found in the Amazon basin and the coastal western Atlantic. Toll-like receptors (TLR) play a key role in recognizing pathogen-associated molecular patterns using leucine-rich repeats (LRRs). We described the diversity of TLR4 and TLR8 genes in these two species of manatee. Amazonian manatee showed seven SNPs in TLR4 and the eight in TLR8, while West Indian manatee shared four and six of those SNPs, respectively. In our analysis, TLR4 showed one non-conservative amino acid replacement substitution in LRR7 and LRR8, on the other hand, TLR8 was less variable and showed only conserved amino acid substitutions. Selection analysis showed that only one TLR4 site was subjected to positive selection and none in TLR8. TLR4 in manatees did not show any evidence of convergent evolution compared to species of the cetacean lineage. Differences in TLR4 and TLR8 polymorphism may be related to distinct selection by pathogens, population reduction of West Indian manatees, or an expected consequence of population expansion in Amazonian manatees. Future studies combining pathogen association and TLR polymorphism may clarify possible roles of these genes and be used for conservation purposes of manatee species.

Environmental factors influencing the abundance of four species of threatened mammals in degraded habitats in the eastern Brazilian Amazon.

On the latest 60 years the degradation and fragmentation of native habitats have been modifying the landscape in the eastern Brazilian Amazon. The adaptive plasticity of an organism has been crucial for its long-term survival and success in these novel ecosystems. In this study, we investigated the response of four endangered species of large terrestrial mammals to the variations in the quality of their original habitats, in a context of high anthropogenic pressure. The distribution of the Myrmecophaga tridactyla (Giant anteater), Priodontes maximus (Giant armadillo), Tapirus terrestris (Lowland tapir) and Tayassu pecari (White-lipped peccary) in all sampled habitats suggests their tolerance to degradation. However, the survival ability of each species in the different habitats was not the same. Among the four species, T. pecari seems to be the one with the least ability to survive in more altered environments. The positive influence of the anthropogenically altered habitats on abundances of three of the four species studied, as observed at the regeneration areas, can be considered as a potential indication of the ecological trap phenomenon. This study reinforces the importance of the forest remnants for the survival of endangered mammal species, in regions of high anthropogenic pressure, as in the eastern Brazilian Amazon.

The Marine Mammal Class II Major Histocompatibility Complex Organization.

Sirenians share with cetaceans and pinnipeds several convergent traits selected for the aquatic lifestyle. Living in water poses new challenges not only for locomotion and feeding but also for combating new pathogens, which may render the immune system one of the best tools aquatic mammals have for dealing with aquatic microbial threats. So far, only cetaceans have had their class II Major Histocompatibility Complex (MHC) organization characterized, despite the importance of MHC genes for adaptive immune responses. This study aims to characterize the organization of the marine mammal class II MHC using publicly available genomes. We located class II sequences in the genomes of one sirenian, four pinnipeds and eight cetaceans using NCBI-BLAST and reannotated the sequences using local BLAST search with exon and intron libraries. Scaffolds containing class II sequences were compared using dotplot analysis and introns were used for phylogenetic analysis. The manatee class II region shares overall synteny with other mammals, however most DR loci were translocated from the canonical location, past the extended class II region. Detailed analysis of the genomes of closely related taxa revealed that this presumed translocation is shared with all other living afrotherians. Other presumptive chromosome rearrangements in Afrotheria are the deletion of DQ loci in Afrosoricida and deletion of DP in E. telfairi. Pinnipeds share the main features of dog MHC: lack of a functional pair of DPA/DPB genes and inverted DRB locus between DQ and DO subregions. All cetaceans share the Cetartiodactyla inversion separating class II genes into two subregions: class IIa, with DR and DQ genes, and class IIb, with non-classic genes and a DRB pseudogene. These results point to three distinct and unheralded class II MHC structures in marine mammals: one canonical organization but lacking DP genes in pinnipeds; one bearing an inversion separating IIa and IIb subregions lacking DP genes found in cetaceans; and one with a translocation separating the most diverse class II gene from the MHC found in afrotherians and presumptive functional DR, DQ, and DP genes. Future functional research will reveal how these aquatic mammals cope with pathogen pressures with these divergent MHC organizations.

The Florida manatee (Trichechus manatus latirostris) T cell receptor loci exhibit V subgroup synteny and chain-specific evolution.

The Florida manatee (Trichechus manatus latirostris) has limited diversity in the immunoglobulin heavy chain. We therefore investigated the antigen receptor loci of the other arm of the adaptive immune system: the T cell receptor. Manatees are the first species from Afrotheria, a basal eutherian superorder, to have an in-depth characterization of all T cell receptor loci. By annotating the genome and expressed transcripts, we found that each chain has distinct features that correlates to their individual functions. The genomic organization also plays a role in modulating sequence conservation between species. There were extensive V subgroup synteny blocks in the TRA and TRB loci between T. m. latirostris and human. Increased genomic locus complexity correlated to increased locus synteny. We also identified evidence for a VHD pseudogene for the first time in a eutherian mammal. These findings emphasize the value of including species within this basal eutherian radiation in comparative studies.

Radiographic evaluation of 19 patients with Paprosky 3A and 3B submitted to acetabular review with trabecular metal wedge / Avaliação radiográfica de 19 pacientes Paprosky 3 A e 3 B submetidos à revisão acetabular com cunha de metal trabeculado

ABSTRACT Objective: This study is aimed at evaluating the fixation of trabecular metal wedges in patients who underwent revision of total hip arthroplasty with large acetabular bone defects. Methods: The radiographs of 19 patients (21 hips), who underwent revision of total hip arthroplasty using trabecular metal wedges from September 2010 to December 2014 were evaluated. This study included only cases of Paprosky 3A and 3B. Preoperative and postoperative images were analyzed. Non-fixation of the implant was defined by the presence of angular variation of the component higher 10 degrees or displacement greater than 6 mm. Patients with follow-up times of less than 24 months or who did not attend the last two appointments were excluded from the study. Results: The mean follow-up time was 39.4 months (25-61). Fixation was achieved in all cases despite its complexity. There was only one case of dislocation that was treated with open reduction. One case developed infection, and was surgically approached on two occasions, with extensive debridement and intravenous antibiotics following protocol, with good evolution. Conclusion: The implanted trabecular metal wedges showed excellent results in the short- and medium-term and may represent another option in the reconstruction of large acetabular defects, sometimes replacing bone reconstruction that uses bone tissue banks or autologous graft.

RESUMO Objetivo: Avaliar a fixação das cunhas de metal trabeculado em pacientes submetidos a revisão de artroplastia do quadril com grandes defeitos ósseos acetabulares. Métodos: Foram avaliadas as radiografias de 19 pacientes, ou 21 quadris, submetidos a revisão de artroplastia do quadril com cunha de metal trabeculado de setembro de 2010 a dezembro de 2014. Foram incluídos somente os casos Paprosky 3 A E 3 B. Exames de imagem pré-operatórios e pós-operatório foram analisados. A não fixação do implante foi definida pela presença de variação angular do componente superior a 10 graus ou deslocamento superior a 6 mm. Pacientes com tempo de seguimento inferior a 24 meses ou aqueles que não compareceram às duas últimas consultas foram excluídos. Resultados: O tempo de seguimento médio foi de 39,4 meses (25-61). A fixação foi alcançada em todos os casos, apesar da complexidade. O único caso de luxação foi submetido a redução aberta. Um caso evoluiu com infecção, foi abordado cirurgicamente em dois momentos, com amplo desbridamento e uso de antibiótico venoso, conforme protocolo, e apresentou boa evolução. Conclusão: O implante em cunha de material trabeculado apresentou resultados excelentes em curto e médio prazos, pode ser mais uma opção nas reconstruções dos grandes defeitos acetabulares, por vezes substitui a reconstrução óssea com o uso de banco de ossos ou enxerto autólogo.

Radiographic evaluation of 19 patients with Paprosky 3A and 3B submitted to acetabular review with trabecular metal wedge.

OBJECTIVE: This study is aimed at evaluating the fixation of trabecular metal wedges in patients who underwent revision of total hip arthroplasty with large acetabular bone defects. METHODS: The radiographs of 19 patients (21 hips), who underwent revision of total hip arthroplasty using trabecular metal wedges from September 2010 to December 2014 were evaluated. This study included only cases of Paprosky 3A and 3B. Preoperative and postoperative images were analyzed. Non-fixation of the implant was defined by the presence of angular variation of the component higher 10 degrees or displacement greater than 6 mm. Patients with follow-up times of less than 24 months or who did not attend the last two appointments were excluded from the study. RESULTS: The mean follow-up time was 39.4 months (25-61). Fixation was achieved in all cases despite its complexity. There was only one case of dislocation that was treated with open reduction. One case developed infection, and was surgically approached on two occasions, with extensive debridement and intravenous antibiotics following protocol, with good evolution. CONCLUSION: The implanted trabecular metal wedges showed excellent results in the short- and medium-term and may represent another option in the reconstruction of large acetabular defects, sometimes replacing bone reconstruction that uses bone tissue banks or autologous graft.

OBJETIVO: Avaliar a fixação das cunhas de metal trabeculado em pacientes submetidos a revisão de artroplastia do quadril com grandes defeitos ósseos acetabulares. MÉTODOS: Foram avaliadas as radiografias de 19 pacientes, ou 21 quadris, submetidos a revisão de artroplastia do quadril com cunha de metal trabeculado de setembro de 2010 a dezembro de 2014. Foram incluídos somente os casos Paprosky 3A E 3B. Exames de imagem pré-operatórios e pós-operatório foram analisados. A não fixação do implante foi definida pela presença de variação angular do componente superior a 10 graus ou deslocamento superior a 6 mm. Pacientes com tempo de seguimento inferior a 24 meses ou aqueles que não compareceram às duas últimas consultas foram excluídos. RESULTADOS: O tempo de seguimento médio foi de 39,4 meses (25-61). A fixação foi alcançada em todos os casos, apesar da complexidade. O único caso de luxação foi submetido a redução aberta. Um caso evoluiu com infecção, foi abordado cirurgicamente em dois momentos, com amplo desbridamento e uso de antibiótico venoso, conforme protocolo, e apresentou boa evolução. CONCLUSÃO: O implante em cunha de material trabeculado apresentou resultados excelentes em curto e médio prazos, pode ser mais uma opção nas reconstruções dos grandes defeitos acetabulares, por vezes substitui a reconstrução óssea com o uso de banco de ossos ou enxerto autólogo.

The Florida manatee (Trichechus manatus latirostris) immunoglobulin heavy chain suggests the importance of clan III variable segments in repertoire diversity.

Manatees are a vulnerable, charismatic sentinel species from the evolutionarily divergent Afrotheria. Manatee health and resistance to infectious disease is of great concern to conservation groups, but little is known about their immune system. To develop manatee-specific tools for monitoring health, we first must have a general knowledge of how the immunoglobulin heavy (IgH) chain locus is organized and transcriptionally expressed. Using the genomic scaffolds of the Florida manatee (Trichechus manatus latirostris), we characterized the potential IgH segmental diversity and constant region isotypic diversity and performed the first Afrotherian repertoire analysis. The Florida manatee has low V(D)J combinatorial diversity (3744 potential combinations) and few constant region isotypes. They also lack clan III V segments, which may have caused reduced VH segment numbers. However, we found productive somatic hypermutation concentrated in the complementarity determining regions. In conclusion, manatees have limited IGHV clan and combinatorial diversity. This suggests that clan III V segments are essential for maintaining IgH locus diversity.

Polymorphic color vision in captive Uta Hick's cuxiús, or bearded sakis (Chiropotes utahickae).

The pitheciines (Chiropotes, Pithecia, and Cacajao) are frugivorous Neotropical primates that specialize on the predation of seeds from unripe fruits, usually cryptic against the foliage. However, little is known about the color vision distribution within this taxon, and even less about the abilities shared by these animals regarding discrimination of chromatic targets. The aim of this study was to evaluate the color vision perception of captive Uta Hick's cuxiús, or bearded sakis (Chiropotes utahickae) through a behavioral paradigm of color visual discrimination, as well as to estimate, by genetic studies, the number and kinds of medium to long wavelength cone photopigment (opsins) encoded by this species. Among 12 cuxiús (7 males and 5 females) studied only 1 female was diagnosed as a trichromat. Results from genotyping were in line with our behavioral data and showed that cuxiús carried one (dichromat) or two (trichromat) medium to long wavelength pigments alleles, demonstrating a color vision polymorphism in C. utahickae similar to the majority of Neotropical Primates.

Polymorphism of DC-SIGN (CD209) promoter in association with clinical symptoms of dengue fever.

C-type lectin DC-SIGN receptor, encoded by CD209, plays a key role in the infection of dendritic cells by dengue virus (DENV). Because the -336A/G SNP (rs4804803) polymorphism in the promoter of CD209 modulates DC-SIGN expression, we investigated the putative association of this polymorphism with DENV infection and its pathogenesis. A control sample of 72 individuals, rigorously selected through a clinical investigation for absence of past dengue fever (DF) was compared to a sample of 168 patients (156 classical DF; 12 dengue hemorrhagic fever), all residents from Pará, Brazil. However, the prevalence of symptoms showed a trend higher in the AA genotype (Wilcoxon test; Z=2.02; p=0.04). Hence, our findings indicate that the G allele downregulates the spectrum of symptoms during the early acute phase of DENV infection, putatively decreasing the viremia, as suggested in the literature.

Expression of PLIN2 and PLIN3 during oocyte maturation and early embryo development in cattle.

In vitro-produced embryos store high lipid content in cytoplasmic lipid droplets (LD), and reduction or removal of LD has been demonstrated to improve freeze-thaw viability. The Perilipin Adipophilin Tail-interacting Protein of 47 kD (PAT) family of proteins is involved in the formation and regulation of LD in many cell types, but their presence has not been addressed either in cattle oocytes or preimplantation embryos. Therefore, this study aimed to detect the expression of PAT family transcripts (Perilipin-2 [PLIN2] and Perilipin-3 [PLIN3]) in immature and in vitro-matured (IVM) oocytes, and in in vitro-produced embryos at the stages of two to four cells, eight to 16 cells, morulae (MO), and blastocyst (BL). The expression of PLIN3 was downregulated in response to IVM, and PLIN2 was comparatively more expressed than PLIN3 in IVM oocytes (P < 0.001). During the early stages of embryo development, PLIN2 expression reached its peak at the MO stage (P < 0.001) and decreased again at the BL stage. In contrast, PLIN3 was expressed in low levels during the earliest stages of development, slightly upregulated at the MO stage (P < 0.05), and greatly increased its expression at the BL stage (15-fold; P < 0.001). PLIN3 was comparatively more expressed than PLIN2 during embryo culture in most stages analyzed (P < 0.05), except in eight- to 16-cell embryos. These results indicate that PLIN2 might be involved in the maintenance of lipid stocks necessary to support embryo development after fertilization of IVM oocytes. Also, we hypothesize that PLIN3 is the main PAT protein responsible for stabilization of LD formed in consequence of the acute lipid load seen during embryo development. We confirmed the presence of both PLIN2 and PLIN3 proteins in BL at Day 7 using immunocytochemistry: these PAT proteins colocalized with LD stained with BODIPY. PLIN3 seemed to be more ubiquitously spread out in the cytoplasm than PLIN2, consistent with the pattern seen in adipocytes. These findings suggest that both elderly (bigger) and newly formed (smaller) LD, positive for PLIN2 and PLIN3 respectively, coexist in blastocysts. To our knowledge this is the first report showing that transcripts of the PAT family are present in cattle oocytes and embryos.

Association of killer cell immunoglobulin-like receptor polymorphisms with chronic hepatitis C and responses to therapy in Brazil.

Soroprevalence for Hepatitis C virus is reported as 2.12% in Northern Brazil, with about 50% of the patients exhibiting a sustained virological response (SVR). Aiming to associate polymorphisms in Killer Cell Immunoglobulin-like Receptors (KIR) with chronic hepatitis C and therapy responses we investigated 125 chronic patients and 345 controls. Additionally, 48 ancestry markers were genotyped to control for population stratification. The frequency of the KIR2DL2 and KIR2DL2+HLA-C(Asp80) gene and ligand was higher in chronic infected patients than in controls (p < 0.0009, OR = 3.4; p = 0.001, OR = 3.45). In fact, KIR2DL3 is a weaker inhibitor of NK activity than KIR2DL2, which could explain the association of KIR2DL2 with chronic infection. Moreover, KIR2DS2 and KIR2DS2+HLA-C(Asp80) (p < 0.0001, OR = 2.51; p = 0.0084, OR = 2.62) and KIR2DS3 (p < 0.0001; OR = 2.57) were associated with chronic infection, independently from KIR2DL2. No differences in ancestry composition were observed between control and patients, even with respect to therapy response groups. The allelic profile KIR2DL2/KIR2DS2/KIR2DS3 was associated with the chronic hepatitis C (p < 0.0001; OR = 3). Furthermore, the patients also showed a higher mean number of activating genes and a lower frequency of the homozygous AA profile, which is likely secondary to the association with non-AA and/or activating genes. In addition, the KIR2DS5 allele was associated with SVR (p = 0.0261; OR = 0.184).The ancestry analysis of samples ruled out any effects of population substructuring and did not evidence interethnic differences in therapy response, as suggested in previous studies.

Predisposition to idiopathic thrombocytopenic purpura maps close to the major histocompatibility complex class I chain-related gene A.

Idiopathic thrombocytopenic purpura (ITP) is an autoimmune condition with poorly known etiology, characterized by platelet destruction. Genetic association studies of this disease are scarce, discrepant, and restricted to major histocompatibility complex (MHC) polymorphisms. Hence, a case-control study was conducted with an aim to map the MHC to IPT susceptibility using HLA-B and nine microsatellite loci encompassing MHC class I, II, and III regions. We compared the allelic frequencies in samples of unrelated healthy controls and ITP patients. After correction for multiple tests, only allele MICA*183, also known as A5.1, demonstrated an association, resulting in the identification of a major predisposing region close to STR-MICA. This result may highlight the putative functional role of MICA in the immune response to ITP.

Amazonian Amerindians exhibit high variability of KIR profiles.

Natural killer cell immunoglobulin-like receptors (KIRs) mediate cell lysis through the recognition of human leukocyte antigen class I complexes in target cells, playing an important role in innate immune response. In this context, disease-based selective pressures could be relevant, leaving signatures detected by population studies. However, most population studies on KIR variability have focused on Europe and Asia, while Americas, Oceania, and Africa remain poorly studied. The aim of this study was to analyze the variability of KIR genes in Amerindian tribes from the Amazon region to infer about their evolutionary history. KIR profiles were estimated in 40 individuals from six Amazonian Amerindian tribes using single specific primer polymerase chain reaction. Twenty-five different profiles were identified, and surprisingly, the haplogroup A frequency was the lowest observed in human populations (16%). Results showed also that KIR variability was higher in this group in contrast to Venezuelan Amerindians. Principal components analysis evidenced that Amerindians formed a separated group from other worldwide populations and showed a higher intraethnic differentiation in comparison to other ethnic groups. Such pattern may reflect small effective size and intense genetic drift. However, because of the role of KIR in immune response, selective pressures cannot be entirely ruled out.

Mitochondrial COII gene sequences provide new insights into the phylogeny of marmoset species groups (Callitrichidae, Primates).

Mitochondrial cytochrome oxidase II (COII) gene sequences (549 base pairs) were used to investigate the taxonomic relationships among 12 marmoset (Callithrix, Cebuella and Mico) taxa. A large number of substitutions were found in the third base codon positions, providing a strong phylogenetic signal in a gene coding a conserved protein. Despite the significant affinity between the 2 Amazonian genera Cebuella and Mico, found in recent molecular studies, the analysis presented here did not resolve convincingly the phylogenetic relationships between the 3 genera. Mico nevertheless formed 3 distinct clades, reflecting a basic division of species groups based on geographic distribution (east or west of the Rio Tapajós) rather than morphology (presence or absence of auricular hair). This supports the taxonomic distinction of the allopatric emiliae forms. In Callithrix, Callithrix aurita forms a distinct clade, but the remaining morphotypes form a somewhat contradictory cluster, possibly resulting from an extremely rapid radiation.

Mitochondrial DNA-like sequence in the nuclear genome of Saguinus (Callitrichinae, Primates): transfer estimation

Seqüências tipo mitocondriais têm comumente sido encontradas no genoma nuclear de diversos organismos. Quando acidentalmente incluídas em estudos de seqüências mitocondriais, diversas conclusöes erröneas podem ser obtidas. No entanto, estes pseudogenes nucleares tipo mitocondriais podem ser usados para a estimativa da taxa relativa de evoluçäo de genes mitocondriais e também como grupo externo em análises filogenéticas. No presente trabalho, seqüências mitocondriais com características do tipo de pseudogene, tais como deleçöes e/ou inserçöes e códons de parada, foram encontradas em tamarins (Saguinus spp., Callitrichinae, Primates). A análise filogenética permitiu a estimativa do tempo da migraçäo da seqüência mitocondrial para o genoma nuclear e algumas inferências filogenéticas. A escolha de um grupo externo näo adequado (Aotus infulatus) näo permitiu uma reconstruçäo filogenética confiável da subfamília Callitrichinae. A divergência bastante antiga de Cebidae (Callitrichinae, Aotinae e Cebinae) pode ter favorecido o aparecimento de homoplasias, obscurecendo a análise.